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-- %TEACHINGWEB%.TaiNg - 20 Nov 2011

Information Content Homework

To implement:

info.pl FILE

I stored a lot of the information in a matrix. if you want to see the matrix, unsupress print in line 191-198

The matrix printed out will be in the form:

SEQUENCE1

SEQUENCE2

SEQUENCE3

Number of A

Number of U

Number of C

Number of G

Number of Gap

Probability of A

Probability of U

" " of C

" " of G

" " of Gap

Entropy

To see the matrix, unsupress line 191-198

To see the joint distribution: Unsupress line 149-1521

To see mutual information, unsupress 170-173

Extra Credit

This 3D graph plots the Column i and Column j number as well as the mutual information shared between them. This is done by MATLAB surface fitting tool. As you can see, the spikes are where the mutual information is highest between the two columns. The peaks are where pairing is most likely to occur because they share the most information in most of the sequences. .

This 2D plot plots Column number versus the entropy of that column. Entropy is lowest when the that area of the sequence is the most conserved. As one can see, the most conserved area is probably position 61-71. Important structures of the tRNA may be encoded there.

I Attachment Action Size Date Who Comment
png Entropy.png manage 74.7 K 2011-11-20 - 23:09 TaiNg
png Mutual.png manage 120.8 K 2011-11-20 - 22:18 TaiNg
txt info.pl.txt manage 7.6 K 2011-11-22 - 05:27 TaiNg Without comment
txt info2.pl.txt manage 7.6 K 2011-11-22 - 05:29 TaiNg With comment
EXT mastertest manage 158.9 K 2011-11-22 - 05:32 TaiNg tRNA test file

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